RNAseq Analysis of Gastric Bacteria in Helicobacter pylori-Associated Carcinogenesis
Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
Helicobacter pylori infects more than half of the world's population, and is known to be involved in several diseases including gastric cancer. Its close interactions with the stomach and host immune system serves as a good model to study the co-adaptation and co-evolution of the organisms in the stomach micro-environment. In this project, we utilized RNA-seq and data analysis tools to investigate differentially expressed genes by H. pylori in patients at different stages of early gastric cancer development. We also investigated the abundance and diversity of bacterial genera other than H. pylori, and looked for correlations with H. pylori presence and number. For differential gene expression of H. pylori, one gene was differentially expressed between samples of corpus atrophy without metaplasia vs. samples of antrum gastritis, and eight genes were found to be differentially expressed between samples of corpus atrophy with metaplasia vs. samples with pan-gastritis. When samples were clustered into different groups based on the expression data, 52 genes (shared or unique to the specific comparison groups) were found to be differentially expressed, but no apparent patterns were observed that could be explained by medical or sample collection data. For bacterial diversity and abundances, we found several genera colonizing the stomach, of which some have been previously identified. While most of these bacteria colonize regardless of the presence of H. pylori, the abundance of three genera, Wolinella, Campylobacter, and Veillonella, seem to be correlated with the presence of H. pylori.
Place, publisher, year, edition, pages
2014. , 33 p.
Bioinformatics and Systems Biology Microbiology
IdentifiersURN: urn:nbn:se:his:diva-9937OAI: oai:DiVA.org:his-9937DiVA: diva2:745501
Subject / course
Bioinformatics - Master’s Programme
2014-06-09, Skövde, 11:00 (English)
Lubovac, Zelmina, Senior Lecturer in BioInformaticsThorell, Kaisa, PhD StudentBengtsson-Palme, Johan, PhD student
Olsson, Björn, Senior Lecturer in BioInformatics